6 Structure Dataset

The structure dataset is probably the most complex of all datasets present in DINO. Its most basic element is the atom. There are two different ways to think about the organization of atoms in this dataset. In one organization, all atoms are in a list and carry properties such as position, name, number, chemical-info (element, charge, vdW-radius), residue-name, residue-number, chain-id, model etc .... Another way is to envision a hierarchy where the structure dataset consists of of or more models, each model consists of one or more chains, each chain consists of one or more residues and each residue is build up from atoms, which carry atom-only properties such as position, chemical-info, name and number.

Most file-formats use the first representation. DINO internaly uses the second way to organize the structural data, but for selection and direct addressing purposes, its easier to think about it in the first way.

Additionally, a trajectory can be loaded into a structure dataset. A trajectory consists of a collection of frames, each with the same set of atoms but different coordinates for each atom (see also below). The trajectory can be played while retaining full interactivity.

element properties shared between dataset and object; modified with .dataset set

aname

X

X

atom name as present in coordinate file

anum

X

X

X

atom number as present in coordinate file

bfac

X

X

X

crystallographic temperature factor (if present)

chain

X

X

alphanumeric chain id

class

X

class of structure: protein, na or misc

ele

X

X

chemical element symbol

model

X

X

X

model number

rname

X

X

residue name as present in coordinate file

rnum

X

X

X

residue number

rtype

X

X

X

residue type: coil (default), helix or strand

weight occ

X

X

weight or crystallographic occupancy (if present)

xyz

X

position of atom

x

X

X

x-coordinate of atom

y

X

X

y-coordinate of atom

z

X

X

z-coordinate of atom

element properties copied from dataset to object, setting on the dataset changes default

color

X

X

color, either a color name or an explicit {r,g,b} triplet

vdwr

X

X

X

X

VdWaals radius

6.1 Structure Objects

New structure objects are created with
new
. There are two object types for the structure dataset:

connect
: Connects atoms with bonds using the chemical connectivity, this is the default object type, all selection properties are considered.

trace
: The central atoms of each residue (
CA
for proteins,
C3'
for nucleic acids) are connected to each other in their sequential order according to residue-numbers. A discontinuity in the residue numbering or a change in chain identifier causes a break in the trace. The selection properties
aname
,
anum
and
ele
have no effect.

NAME
defaults to the dataset name.
TYPE
defaults to
connect
. Object properties that can be set are listed in Table 8 (P. 27). A selection with selectable atom properties (column L in Table 9 (P. 28)) can be given.

grab reset fix center
: transformation related commands (see "5.1.8 Transformation" on page 25)
; reset
additionally can have the parameters
all
(default) or
center
, the latter will set the center of rotation back to the center of geometry after a modification with
scene set center

6.3 Structure Object Commands

Structure object commands are issued as:

Syntax: .struct.obj command [parameters]

Following is a list of all structure object commands:

renew
: Similar to dataset command
new
, except the type and name are already determined, so only selection and setting is possible. If either selection or setting (or both) are omitted, the current selection resp. setting is maintained (see "5.1.5 Modifying Objects" on page 23).

Syntax: .struct.obj renew [-selection SEL] [-set SET]

show hide
: turns display of the object in the graphics window on or off. Identical to clicking on the object name in the object menu (see "4.12 The GUI" on page 20).

Syntax: .struct.obj show
.struct.obj hide

clear
: removes all labels. Hint: use
.struct.* clear
to get rid of all labels.

6.4 Structure Element Commands

The format of ELEMENT depends on the dataset itself, to be more precise whether chain and/or model are present. The general format is

ELEMENT = [model.][chain.][rnum.]aname

model
,
chain
and
rnum
are only required if the structure dataset contains different models, chains and/or residues. The atom name is case sensitive and must be entered as present in the coordinate file.

6.5 Connectivity

auto-connectivity

As mentioned above, a structure dataset is automatically created when loading a file which contains coordinate-data. Although most coordinate-files do not contain explicit connectivity information, the connectivity is implicitly given by:

The relationships between atoms as defined by chain-id, residue-number, residue-name and atom-name

The distance between two atoms, which is different for bonded atoms and atoms in vdW contact.

DINO uses an auto-connectivity routine that exploits both implicit and explicit connectivity rules. It contains an internal connectivity table for the 20 amino-acids and the 5 bases, including a rule which atoms connect residues n and n+17 . If an atom is encountered that is not defined by the internal connectivity table, it is connected to all atoms that lie within CUTOFF of its position; where CUTOFF is defined as the sum of the two van der Waals radii divided by two. Additionally, connectivity defined in the coordinate-file is considered (e.g. CONECT in PDB). As a consequence, disulfide bridges must be either explicitely defined with CONECT, or the atom name of the cystein sulfur (normally SG) must be changed to force distance-based connectivity (e.g. into SS).

manual connectivity

The structure dataset command
connect
can be utilized to connect two atoms together

Syntax: .struct connect ELEMENT1 ELEMENT2

ELEMENT
is a structure dataset element in the form as explained in the direct access section above.

Example: .struct connect A.13.SG B.156.SG

6.6 Trajectories

Trajectories are an addition to a structure dataset. They provide a collection of frames which contain new coordinates for each atom of the structure dataset. First a trajectory needs to be loaded from a file

Syntax: .struct load file.ext [-type T] [-swap]

If the type is not given, it is guessed from the extension. Currently, CHARMM (extension
.trj
type
charmm
) and CNS (extension
.crd
, type
cns
) trajectories are supported The parameter
-swap
can be used to apply byte-order swapping to the trajectory.

Once trajectories are loaded, they can be played continuously or each frame can be looked at one by one.

wait
denotes the number of wait-cycles until the next frame is displayed, default is 0.
begin
and
end
specify from which to which frame the trajectory shall run, default is 1 to max.
mode
can be
loop
(default) or
rock
.

While the trajectory is playing, full interactivity is available.

The structure dataset property
tfast
can be used to turn off the recalculation of internal parameters needed for render mode custom. This will considerably speed up trajectory display, but will only work if all structure dataset objects are not in render mode
custom
. This flag is true (fast trajectory) per default.

6.7 Render & Graphical Appearance

The command
render
modifies the graphical appearance of an object:

Syntax: .struct.obj render PV [,PV ...]

The render properties applicable to the structure dataset objects are given in Table 11 (P. 33). Depending on the type of object (connect or trace), several rendering modes are available, specified as

Syntax: .struct.obj render MODE

Modes:

simple
(default mode for
connect
and
trace
): bonds are drawn as lines with width
linew
, each half colored according to the color of the connecting atom.

custom
(
connect
and
trace
): bonds are drawn as cylinders with width
bw
, atoms are drawn as spheres with radius
sr

cpk
(
connect
): atoms are displayed as spheres with a radius of their
vdwr

hsc
(
trace
):secondary structure rendering of protein or dna trace; a continuous spline with interpolation runs exactly through the atom positions.protein rendering: coils as tubes of radius bw and axial ratio of tuber, helices with width helixw and thickness helixt, and strands with width strandw and thickness strandtdna rendering: backbone as tubes of radius bw and axial ratio of tuber, purines and pyrimidines are cartoonlike displayed with approximate tilting of the sugar and the base